ArticleSignal transduction and targeted therapy2021
Metagenomic analysis reveals oropharyngeal microbiota alterations in patients with COVID-19.
Article in Signal transduction and targeted therapy, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Perturbations in gut and respiratory microbiota in COVID-19 and influenza patients: a systematic review and meta-analysis.Frontiers in medicine · 2024Pooled it
- Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Trial
- Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.Microbiology spectrum · 2026Article
- Organ cross-talk: molecular mechanisms, biological functions, and therapeutic interventions for diseases.Signal transduction and targeted therapy · 2026Review
- Epidemiological characteristics and co-occurrence patterns ofJournal of oral microbiology · 2026Article
- SARS-CoV-2 lineages and naso-oropharyngeal bacterial communities in COVID-19 reinfection: A study in West Java, Indonesia.Narra J · 2025Article
- Multi-omics analysis reveals disrupted gut microbiota and metabolism in gastric cancer patients with high SIRI.BMC cancer · 2025Article
- Oral microbiota and respiratory diseases: advances and perspectives.Clinical microbiology reviews · 2025Review
- Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.Communications biology · 2025Article
- Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.Microorganisms · 2025Article
- DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.Genome biology · 2025Article
- Natural Infection of Omicron BA.5.2 in Patients Provides Broad Immune Responses Against SARS-CoV-2.Microorganisms · 2025Article
- Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.Scientific reports · 2025Article
- The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19.eLife · 2025Observational
- Article
- Pathogenic and periodontal bacteria may contribute to the fatal outcome of critically ill elderly COVID-19 patients.Scientific reports · 2025Article
- Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.Journal of oral microbiology · 2025Article
- Respiratory microbiota, host immunity, respiratory viral infections and malignant tumors.Frontiers in microbiology · 2025Review
- Unraveling salivary microbiota diversity following kidney transplantation: insights from baseline peripheral blood lymphocyte subsets.Journal of oral microbiology · 2025Article
- Major alteration of lung microbiome and the host responses in critically ill COVID-19 patients with high viral load.Scientific reports · 2024Article
34 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
Abstract
COVID-19 remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by shotgun metagenomic sequencing analyses of oropharynx swab specimens from 31 COVID-19 patients, 29 influenza B patients, and 28 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in the COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Veillonella and Megasphaera and depletion of Pseudopropionibacterium, Rothia, and Streptococcus. Based on the relative abundance of the oropharyngeal microbiome, we built a microbial classifier to distinguish COVID-19 patients from flu patients and healthy controls with an AUC of 0.889, in which Veillonella was identified as the most prominent biomarker for COVID-19 group. Several members of the genus Veillonella, especially Veillonella parvula which was highly enriched in the oropharynx of our COVID-19 patients, were also overrepresented in the BALF of COVID-19 patients, indicating that the oral cavity acts as a natural reservoir for pathogens to induce co-infections in the lungs of COVID-19 patients. We also found the increased ratios of Klebsiella sp., Acinetobacter sp., and Serratia sp. were correlated with both disease severity and elevated systemic inflammation markers (neutrophil-lymphocyte ratio, NLR), suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the inflammatory response. Moreover, the oropharyngeal microbiome of COVID-19 patients exhibited a significant enrichment in amino acid metabolism and xenobiotic biodegradation and metabolism. In addition, all 26 drug classes of antimicrobial resistance genes were detected in the COVID-19 group, and were significantly enriched in critical cases. In conclusion, we found that oropharyngeal microbiota alterations and functional differences were associated with COVID-19 severity.
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